Starting phenix.real_space_refine on Wed Sep 17 23:49:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dg3_46822/09_2025/9dg3_46822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dg3_46822/09_2025/9dg3_46822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dg3_46822/09_2025/9dg3_46822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dg3_46822/09_2025/9dg3_46822.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dg3_46822/09_2025/9dg3_46822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dg3_46822/09_2025/9dg3_46822.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 292 5.49 5 S 17 5.16 5 C 6967 2.51 5 N 2342 2.21 5 O 2934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12553 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 773 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3015 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2971 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "M" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 249 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 32} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "N" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 405 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 3, 'TRANS': 68} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 2, 'GLU:plan': 6, 'ASP:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11931 SG CYS M 27 29.583 48.634 68.684 1.00205.57 S ATOM 11950 SG CYS M 30 27.941 45.395 67.355 1.00208.97 S ATOM 12028 SG CYS M 41 29.688 45.285 70.695 1.00205.36 S ATOM 12048 SG CYS M 44 31.653 45.682 67.608 1.00195.86 S Time building chain proxies: 2.77, per 1000 atoms: 0.22 Number of scatterers: 12553 At special positions: 0 Unit cell: (103.024, 118.368, 122.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 17 16.00 P 292 15.00 O 2934 8.00 N 2342 7.00 C 6967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 376.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 301 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 44 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 30 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 41 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 27 " Number of angles added : 6 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1616 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 65.6% alpha, 4.2% beta 143 base pairs and 253 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.103A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.620A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.313A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.583A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 35 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.810A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.472A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.684A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.470A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'M' and resid 25 through 26 Processing sheet with id=AB2, first strand: chain 'N' and resid 12 through 16 436 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 726 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 253 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2848 1.34 - 1.46: 4190 1.46 - 1.58: 5715 1.58 - 1.70: 582 1.70 - 1.82: 27 Bond restraints: 13362 Sorted by residual: bond pdb=" C PHE E 84 " pdb=" N GLN E 85 " ideal model delta sigma weight residual 1.330 1.377 -0.047 1.38e-02 5.25e+03 1.17e+01 bond pdb=" N ILE D 51 " pdb=" CA ILE D 51 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N ASN C 73 " pdb=" CA ASN C 73 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.12e-02 7.97e+03 9.60e+00 bond pdb=" N VAL B 57 " pdb=" CA VAL B 57 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.19e+00 bond pdb=" N VAL B 21 " pdb=" CA VAL B 21 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 9.16e+00 ... (remaining 13357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 18804 2.15 - 4.30: 451 4.30 - 6.45: 57 6.45 - 8.60: 13 8.60 - 10.75: 4 Bond angle restraints: 19329 Sorted by residual: angle pdb=" N GLN B 27 " pdb=" CA GLN B 27 " pdb=" C GLN B 27 " ideal model delta sigma weight residual 114.16 103.58 10.58 1.48e+00 4.57e-01 5.11e+01 angle pdb=" CB LYS G 36 " pdb=" CG LYS G 36 " pdb=" CD LYS G 36 " ideal model delta sigma weight residual 111.30 122.05 -10.75 2.30e+00 1.89e-01 2.19e+01 angle pdb=" CB LYS G 13 " pdb=" CG LYS G 13 " pdb=" CD LYS G 13 " ideal model delta sigma weight residual 111.30 121.28 -9.98 2.30e+00 1.89e-01 1.88e+01 angle pdb=" N ASN C 73 " pdb=" CA ASN C 73 " pdb=" C ASN C 73 " ideal model delta sigma weight residual 112.97 108.61 4.36 1.06e+00 8.90e-01 1.69e+01 angle pdb=" CA ARG G 99 " pdb=" CB ARG G 99 " pdb=" CG ARG G 99 " ideal model delta sigma weight residual 114.10 122.21 -8.11 2.00e+00 2.50e-01 1.64e+01 ... (remaining 19324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.16: 5268 26.16 - 52.32: 1606 52.32 - 78.48: 382 78.48 - 104.64: 10 104.64 - 130.79: 2 Dihedral angle restraints: 7268 sinusoidal: 4772 harmonic: 2496 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 158.85 21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ILE B 26 " pdb=" C ILE B 26 " pdb=" N GLN B 27 " pdb=" CA GLN B 27 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C4' DC I 128 " pdb=" C3' DC I 128 " pdb=" O3' DC I 128 " pdb=" P DT I 129 " ideal model delta sinusoidal sigma weight residual 220.00 89.21 130.79 1 3.50e+01 8.16e-04 1.30e+01 ... (remaining 7265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2169 0.108 - 0.216: 57 0.216 - 0.324: 0 0.324 - 0.431: 0 0.431 - 0.539: 3 Chirality restraints: 2229 Sorted by residual: chirality pdb=" P DA J 151 " pdb=" OP1 DA J 151 " pdb=" OP2 DA J 151 " pdb=" O5' DA J 151 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" P DG J 152 " pdb=" OP1 DG J 152 " pdb=" OP2 DG J 152 " pdb=" O5' DG J 152 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" P DA J 153 " pdb=" OP1 DA J 153 " pdb=" OP2 DA J 153 " pdb=" O5' DA J 153 " both_signs ideal model delta sigma weight residual True 2.35 -2.85 -0.50 2.00e-01 2.50e+01 6.29e+00 ... (remaining 2226 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " -0.036 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CG TYR B 88 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 71 " 0.271 9.50e-02 1.11e+02 1.21e-01 9.07e+00 pdb=" NE ARG C 71 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 71 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 71 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 71 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 80 " -0.022 2.00e-02 2.50e+03 2.08e-02 8.65e+00 pdb=" CG TYR H 80 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR H 80 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR H 80 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR H 80 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR H 80 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR H 80 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR H 80 " -0.009 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 902 2.73 - 3.27: 11782 3.27 - 3.81: 25710 3.81 - 4.36: 28992 4.36 - 4.90: 41823 Nonbonded interactions: 109209 Sorted by model distance: nonbonded pdb=" O LEU G 85 " pdb=" OD1 ASN G 89 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 68 " model vdw 2.220 3.040 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 75 " model vdw 2.250 3.040 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 75 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR G 39 " pdb=" OE1 GLU H 68 " model vdw 2.288 3.040 ... (remaining 109204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 40 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 134)) } ncs_group { reference = (chain 'B' and resid 23 through 101) selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 117)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 117)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.520 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13366 Z= 0.256 Angle : 0.791 10.752 19335 Z= 0.474 Chirality : 0.046 0.539 2229 Planarity : 0.007 0.121 1440 Dihedral : 28.102 130.794 5652 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.15 % Allowed : 22.19 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.28), residues: 840 helix: 1.54 (0.22), residues: 555 sheet: 1.21 (1.10), residues: 25 loop : -0.35 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 96 TYR 0.052 0.003 TYR B 88 PHE 0.012 0.002 PHE B 100 TRP 0.009 0.002 TRP M 25 HIS 0.008 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00491 (13362) covalent geometry : angle 0.78925 (19329) hydrogen bonds : bond 0.06810 ( 803) hydrogen bonds : angle 4.12141 ( 2016) metal coordination : bond 0.01028 ( 4) metal coordination : angle 3.15875 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: F 74 GLU cc_start: 0.9157 (tp30) cc_final: 0.8728 (tp30) REVERT: H 31 LYS cc_start: 0.8831 (ttpp) cc_final: 0.8516 (pttm) REVERT: H 65 ASP cc_start: 0.9228 (t0) cc_final: 0.9027 (t0) REVERT: H 80 TYR cc_start: 0.8323 (m-80) cc_final: 0.7947 (m-80) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1183 time to fit residues: 29.4374 Evaluate side-chains 158 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.0970 chunk 106 optimal weight: 0.4980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.055059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.040481 restraints weight = 73507.917| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.93 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13366 Z= 0.173 Angle : 0.625 11.711 19335 Z= 0.365 Chirality : 0.036 0.157 2229 Planarity : 0.005 0.057 1440 Dihedral : 30.583 129.620 4132 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.52 % Allowed : 19.91 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.28), residues: 840 helix: 1.75 (0.22), residues: 557 sheet: 1.12 (1.12), residues: 25 loop : -0.38 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 76 TYR 0.053 0.002 TYR B 88 PHE 0.016 0.001 PHE B 61 TRP 0.005 0.001 TRP M 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00377 (13362) covalent geometry : angle 0.62405 (19329) hydrogen bonds : bond 0.04812 ( 803) hydrogen bonds : angle 3.61767 ( 2016) metal coordination : bond 0.00918 ( 4) metal coordination : angle 2.11881 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8578 (tp30) cc_final: 0.8313 (tm-30) REVERT: C 100 VAL cc_start: 0.9625 (t) cc_final: 0.9280 (p) REVERT: D 65 ASP cc_start: 0.9048 (t0) cc_final: 0.8789 (t0) REVERT: D 80 TYR cc_start: 0.8060 (m-80) cc_final: 0.7747 (m-10) REVERT: F 53 GLU cc_start: 0.9330 (tp30) cc_final: 0.8879 (mm-30) REVERT: H 31 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8462 (pttm) REVERT: H 65 ASP cc_start: 0.9150 (t0) cc_final: 0.8910 (t0) REVERT: H 68 GLU cc_start: 0.8974 (tp30) cc_final: 0.8658 (tp30) REVERT: H 80 TYR cc_start: 0.8017 (m-10) cc_final: 0.7700 (m-80) outliers start: 10 outliers final: 6 residues processed: 175 average time/residue: 0.1190 time to fit residues: 29.3951 Evaluate side-chains 165 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain M residue 50 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 102 optimal weight: 0.0370 chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 0.0000 chunk 52 optimal weight: 0.6980 chunk 104 optimal weight: 50.0000 chunk 12 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.055537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.040818 restraints weight = 73626.833| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.16 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13366 Z= 0.153 Angle : 0.585 6.514 19335 Z= 0.347 Chirality : 0.035 0.185 2229 Planarity : 0.005 0.056 1440 Dihedral : 30.344 126.341 4132 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.98 % Allowed : 19.45 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.28), residues: 840 helix: 1.95 (0.22), residues: 562 sheet: 1.31 (1.11), residues: 25 loop : -0.40 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 76 TYR 0.020 0.002 TYR D 80 PHE 0.009 0.001 PHE E 78 TRP 0.003 0.001 TRP M 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00327 (13362) covalent geometry : angle 0.58437 (19329) hydrogen bonds : bond 0.04094 ( 803) hydrogen bonds : angle 3.32192 ( 2016) metal coordination : bond 0.00669 ( 4) metal coordination : angle 2.00322 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: B 54 THR cc_start: 0.9576 (m) cc_final: 0.9164 (p) REVERT: C 64 GLU cc_start: 0.8798 (tp30) cc_final: 0.8363 (tm-30) REVERT: C 90 ASP cc_start: 0.8125 (t0) cc_final: 0.7609 (t0) REVERT: D 43 LYS cc_start: 0.9358 (mmtm) cc_final: 0.8946 (tppt) REVERT: D 65 ASP cc_start: 0.9221 (t0) cc_final: 0.8935 (t0) REVERT: D 76 ARG cc_start: 0.9340 (ttm110) cc_final: 0.9040 (ttp-110) REVERT: D 83 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8475 (tpp80) REVERT: E 76 GLN cc_start: 0.8929 (mp10) cc_final: 0.8645 (mp10) REVERT: E 125 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.8817 (mp10) REVERT: F 74 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8907 (mm-30) REVERT: G 39 TYR cc_start: 0.8362 (m-80) cc_final: 0.8103 (m-80) REVERT: G 94 ASN cc_start: 0.9430 (t0) cc_final: 0.9193 (t0) REVERT: H 31 LYS cc_start: 0.8773 (ttpp) cc_final: 0.8408 (pttm) REVERT: H 65 ASP cc_start: 0.9293 (t0) cc_final: 0.9015 (t0) REVERT: H 68 GLU cc_start: 0.9178 (tp30) cc_final: 0.8892 (tp30) outliers start: 13 outliers final: 7 residues processed: 187 average time/residue: 0.1251 time to fit residues: 31.9967 Evaluate side-chains 166 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain H residue 106 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 98 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.053711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.038879 restraints weight = 73315.659| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.96 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13366 Z= 0.205 Angle : 0.601 7.182 19335 Z= 0.354 Chirality : 0.036 0.165 2229 Planarity : 0.005 0.053 1440 Dihedral : 30.221 124.192 4132 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.04 % Allowed : 20.52 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.29), residues: 840 helix: 2.18 (0.22), residues: 562 sheet: 1.41 (1.14), residues: 25 loop : -0.37 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 55 TYR 0.024 0.002 TYR F 88 PHE 0.012 0.001 PHE E 104 TRP 0.008 0.005 TRP M 25 HIS 0.005 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00459 (13362) covalent geometry : angle 0.59892 (19329) hydrogen bonds : bond 0.05015 ( 803) hydrogen bonds : angle 3.33747 ( 2016) metal coordination : bond 0.01075 ( 4) metal coordination : angle 2.79140 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.9044 (tmtt) REVERT: C 64 GLU cc_start: 0.8756 (tp30) cc_final: 0.8337 (tm-30) REVERT: C 90 ASP cc_start: 0.8300 (t0) cc_final: 0.8005 (t0) REVERT: D 43 LYS cc_start: 0.9364 (mmtm) cc_final: 0.8943 (tppt) REVERT: D 65 ASP cc_start: 0.9120 (t0) cc_final: 0.8830 (t0) REVERT: D 85 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8980 (p) REVERT: D 90 GLU cc_start: 0.8390 (mp0) cc_final: 0.8177 (mp0) REVERT: E 76 GLN cc_start: 0.8837 (mp10) cc_final: 0.8565 (mp10) REVERT: F 25 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8465 (t0) REVERT: G 92 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: G 94 ASN cc_start: 0.9469 (t0) cc_final: 0.8841 (m-40) REVERT: H 65 ASP cc_start: 0.9256 (t0) cc_final: 0.8970 (t0) REVERT: H 68 GLU cc_start: 0.9120 (tp30) cc_final: 0.8796 (tp30) REVERT: H 80 TYR cc_start: 0.8297 (m-80) cc_final: 0.8085 (m-80) outliers start: 20 outliers final: 8 residues processed: 171 average time/residue: 0.1143 time to fit residues: 27.3978 Evaluate side-chains 165 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 92 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 25 ASN F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.053807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.038790 restraints weight = 72567.429| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.96 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13366 Z= 0.167 Angle : 0.589 9.854 19335 Z= 0.345 Chirality : 0.035 0.180 2229 Planarity : 0.004 0.053 1440 Dihedral : 30.255 121.278 4132 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.58 % Allowed : 22.04 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.29), residues: 840 helix: 2.16 (0.22), residues: 564 sheet: 1.41 (1.16), residues: 25 loop : -0.35 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 67 TYR 0.022 0.002 TYR B 88 PHE 0.008 0.001 PHE E 104 TRP 0.003 0.001 TRP M 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00364 (13362) covalent geometry : angle 0.58740 (19329) hydrogen bonds : bond 0.04165 ( 803) hydrogen bonds : angle 3.16016 ( 2016) metal coordination : bond 0.00795 ( 4) metal coordination : angle 2.28315 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9219 (ptmm) cc_final: 0.8933 (tmtt) REVERT: B 92 ARG cc_start: 0.9416 (OUTLIER) cc_final: 0.8587 (tmm-80) REVERT: C 64 GLU cc_start: 0.8804 (tp30) cc_final: 0.8457 (tm-30) REVERT: C 90 ASP cc_start: 0.8099 (t0) cc_final: 0.7801 (t0) REVERT: D 43 LYS cc_start: 0.9391 (mmtm) cc_final: 0.9026 (tppt) REVERT: D 65 ASP cc_start: 0.9208 (t0) cc_final: 0.8948 (t0) REVERT: D 90 GLU cc_start: 0.8446 (mp0) cc_final: 0.8192 (mp0) REVERT: E 76 GLN cc_start: 0.8743 (mp10) cc_final: 0.8395 (mp10) REVERT: F 25 ASN cc_start: 0.8976 (OUTLIER) cc_final: 0.8296 (t0) REVERT: F 92 ARG cc_start: 0.9369 (mtp-110) cc_final: 0.9038 (ttp80) REVERT: H 65 ASP cc_start: 0.9339 (t0) cc_final: 0.9056 (t0) REVERT: H 68 GLU cc_start: 0.9199 (tp30) cc_final: 0.8955 (tp30) outliers start: 17 outliers final: 9 residues processed: 179 average time/residue: 0.1150 time to fit residues: 28.6531 Evaluate side-chains 165 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain M residue 50 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.051758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.036070 restraints weight = 74613.470| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.95 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 13366 Z= 0.268 Angle : 0.641 8.225 19335 Z= 0.371 Chirality : 0.037 0.199 2229 Planarity : 0.005 0.051 1440 Dihedral : 30.384 119.571 4132 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.34 % Allowed : 21.12 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.29), residues: 840 helix: 2.21 (0.22), residues: 562 sheet: 2.32 (1.23), residues: 21 loop : -0.52 (0.35), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.027 0.003 TYR B 88 PHE 0.011 0.001 PHE C 25 TRP 0.008 0.002 TRP M 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00598 (13362) covalent geometry : angle 0.63867 (19329) hydrogen bonds : bond 0.05517 ( 803) hydrogen bonds : angle 3.40776 ( 2016) metal coordination : bond 0.01520 ( 4) metal coordination : angle 3.18943 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9019 (tmtt) REVERT: B 92 ARG cc_start: 0.9435 (OUTLIER) cc_final: 0.8594 (tmm-80) REVERT: C 64 GLU cc_start: 0.8779 (tp30) cc_final: 0.8459 (tm-30) REVERT: C 90 ASP cc_start: 0.8261 (t0) cc_final: 0.7785 (t0) REVERT: D 43 LYS cc_start: 0.9379 (mmtm) cc_final: 0.9027 (tppt) REVERT: D 65 ASP cc_start: 0.9159 (t0) cc_final: 0.8867 (t0) REVERT: D 76 ARG cc_start: 0.9218 (ttp-110) cc_final: 0.9011 (ttp-110) REVERT: D 90 GLU cc_start: 0.8476 (mp0) cc_final: 0.8174 (mp0) REVERT: F 25 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8668 (t0) REVERT: G 39 TYR cc_start: 0.8467 (m-80) cc_final: 0.8005 (m-80) REVERT: G 92 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: G 94 ASN cc_start: 0.9461 (OUTLIER) cc_final: 0.9050 (m-40) REVERT: H 65 ASP cc_start: 0.9285 (t0) cc_final: 0.8996 (t0) REVERT: H 68 GLU cc_start: 0.9133 (tp30) cc_final: 0.8677 (tp30) REVERT: H 90 GLU cc_start: 0.8863 (mp0) cc_final: 0.8508 (mp0) REVERT: H 102 GLU cc_start: 0.8069 (tp30) cc_final: 0.7762 (tp30) outliers start: 22 outliers final: 13 residues processed: 165 average time/residue: 0.1253 time to fit residues: 28.4615 Evaluate side-chains 162 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 50 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 109 optimal weight: 30.0000 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 46 HIS H 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.053091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.037970 restraints weight = 72770.886| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.85 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13366 Z= 0.166 Angle : 0.611 9.540 19335 Z= 0.354 Chirality : 0.035 0.185 2229 Planarity : 0.004 0.052 1440 Dihedral : 30.395 117.675 4132 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.19 % Allowed : 23.56 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.29), residues: 840 helix: 2.18 (0.22), residues: 564 sheet: 2.52 (1.25), residues: 21 loop : -0.50 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 52 TYR 0.043 0.002 TYR F 88 PHE 0.007 0.001 PHE E 78 TRP 0.005 0.001 TRP M 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00363 (13362) covalent geometry : angle 0.60947 (19329) hydrogen bonds : bond 0.04347 ( 803) hydrogen bonds : angle 3.24769 ( 2016) metal coordination : bond 0.00825 ( 4) metal coordination : angle 2.25927 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8953 (tmtt) REVERT: B 63 GLU cc_start: 0.8732 (tt0) cc_final: 0.8246 (tt0) REVERT: B 92 ARG cc_start: 0.9428 (OUTLIER) cc_final: 0.8567 (tmm-80) REVERT: C 64 GLU cc_start: 0.8808 (tp30) cc_final: 0.8576 (tm-30) REVERT: D 43 LYS cc_start: 0.9364 (mmtm) cc_final: 0.8982 (tppt) REVERT: D 65 ASP cc_start: 0.9210 (t0) cc_final: 0.8951 (t0) REVERT: D 90 GLU cc_start: 0.8495 (mp0) cc_final: 0.8103 (mp0) REVERT: E 76 GLN cc_start: 0.9107 (mt0) cc_final: 0.8786 (mp10) REVERT: F 25 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8493 (t0) REVERT: F 53 GLU cc_start: 0.9318 (tp30) cc_final: 0.9043 (mm-30) REVERT: F 92 ARG cc_start: 0.9418 (OUTLIER) cc_final: 0.9066 (ttp80) REVERT: G 39 TYR cc_start: 0.8465 (m-80) cc_final: 0.8198 (m-80) REVERT: G 92 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: G 94 ASN cc_start: 0.9340 (OUTLIER) cc_final: 0.8896 (m-40) REVERT: H 65 ASP cc_start: 0.9213 (t0) cc_final: 0.8964 (t0) REVERT: H 68 GLU cc_start: 0.9154 (tp30) cc_final: 0.8854 (tp30) REVERT: H 102 GLU cc_start: 0.8021 (tp30) cc_final: 0.7580 (tp30) REVERT: H 106 HIS cc_start: 0.7896 (OUTLIER) cc_final: 0.7671 (m170) outliers start: 21 outliers final: 11 residues processed: 174 average time/residue: 0.1194 time to fit residues: 28.6596 Evaluate side-chains 173 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain M residue 50 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 46 HIS H 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.050967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.035689 restraints weight = 74280.122| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.93 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 13366 Z= 0.316 Angle : 0.676 9.519 19335 Z= 0.386 Chirality : 0.038 0.188 2229 Planarity : 0.005 0.051 1440 Dihedral : 30.430 117.609 4132 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.50 % Allowed : 24.32 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.29), residues: 840 helix: 2.11 (0.22), residues: 562 sheet: 2.42 (1.23), residues: 21 loop : -0.67 (0.35), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 52 TYR 0.030 0.003 TYR H 80 PHE 0.008 0.001 PHE A 104 TRP 0.010 0.003 TRP M 25 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00705 (13362) covalent geometry : angle 0.67384 (19329) hydrogen bonds : bond 0.05875 ( 803) hydrogen bonds : angle 3.54825 ( 2016) metal coordination : bond 0.01602 ( 4) metal coordination : angle 3.43731 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.9003 (tmtt) REVERT: B 63 GLU cc_start: 0.8803 (tt0) cc_final: 0.8286 (tt0) REVERT: C 64 GLU cc_start: 0.8890 (tp30) cc_final: 0.8655 (tm-30) REVERT: D 43 LYS cc_start: 0.9361 (mmtm) cc_final: 0.8975 (tppt) REVERT: D 90 GLU cc_start: 0.8536 (mp0) cc_final: 0.8100 (mp0) REVERT: F 25 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8380 (t0) REVERT: G 39 TYR cc_start: 0.8600 (m-80) cc_final: 0.7981 (m-80) REVERT: G 92 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8266 (mt-10) REVERT: G 94 ASN cc_start: 0.9372 (OUTLIER) cc_final: 0.8948 (m-40) REVERT: H 65 ASP cc_start: 0.9350 (t0) cc_final: 0.9053 (t0) REVERT: H 68 GLU cc_start: 0.9197 (tp30) cc_final: 0.8657 (tp30) REVERT: H 90 GLU cc_start: 0.8964 (mp0) cc_final: 0.8611 (mp0) REVERT: H 102 GLU cc_start: 0.8136 (tp30) cc_final: 0.7665 (tp30) outliers start: 23 outliers final: 13 residues processed: 161 average time/residue: 0.1154 time to fit residues: 25.8920 Evaluate side-chains 159 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.051945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.036829 restraints weight = 73800.288| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.92 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13366 Z= 0.199 Angle : 0.643 10.296 19335 Z= 0.367 Chirality : 0.036 0.203 2229 Planarity : 0.004 0.051 1440 Dihedral : 30.465 115.785 4132 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.74 % Allowed : 25.53 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.29), residues: 840 helix: 2.09 (0.22), residues: 564 sheet: 2.59 (1.26), residues: 21 loop : -0.64 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.045 0.003 TYR F 88 PHE 0.007 0.001 PHE B 61 TRP 0.006 0.002 TRP M 25 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00444 (13362) covalent geometry : angle 0.64102 (19329) hydrogen bonds : bond 0.04635 ( 803) hydrogen bonds : angle 3.35068 ( 2016) metal coordination : bond 0.01018 ( 4) metal coordination : angle 2.56919 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8936 (tmtt) REVERT: B 63 GLU cc_start: 0.8793 (tt0) cc_final: 0.8280 (tt0) REVERT: C 64 GLU cc_start: 0.8853 (tp30) cc_final: 0.8639 (tm-30) REVERT: D 43 LYS cc_start: 0.9333 (mmtm) cc_final: 0.8949 (tppt) REVERT: D 65 ASP cc_start: 0.9192 (t0) cc_final: 0.8935 (t0) REVERT: D 90 GLU cc_start: 0.8538 (mp0) cc_final: 0.8109 (mp0) REVERT: E 76 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8873 (mp10) REVERT: F 25 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8526 (t0) REVERT: F 92 ARG cc_start: 0.9473 (OUTLIER) cc_final: 0.9075 (ttp80) REVERT: G 39 TYR cc_start: 0.8593 (m-80) cc_final: 0.7987 (m-80) REVERT: G 92 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: H 65 ASP cc_start: 0.9229 (t0) cc_final: 0.8987 (t0) REVERT: H 68 GLU cc_start: 0.9143 (tp30) cc_final: 0.8612 (tp30) REVERT: H 90 GLU cc_start: 0.8934 (mp0) cc_final: 0.8544 (mp0) REVERT: H 102 GLU cc_start: 0.7963 (tp30) cc_final: 0.7592 (tp30) outliers start: 18 outliers final: 12 residues processed: 165 average time/residue: 0.1230 time to fit residues: 27.9352 Evaluate side-chains 166 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 98 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.051454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.036291 restraints weight = 74322.207| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.91 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13366 Z= 0.234 Angle : 0.655 10.406 19335 Z= 0.373 Chirality : 0.036 0.209 2229 Planarity : 0.004 0.050 1440 Dihedral : 30.406 115.480 4132 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.04 % Allowed : 24.92 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.28), residues: 840 helix: 2.15 (0.22), residues: 562 sheet: 0.71 (1.51), residues: 12 loop : -0.61 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.027 0.002 TYR H 80 PHE 0.006 0.001 PHE D 67 TRP 0.008 0.002 TRP M 25 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00523 (13362) covalent geometry : angle 0.65307 (19329) hydrogen bonds : bond 0.05011 ( 803) hydrogen bonds : angle 3.41320 ( 2016) metal coordination : bond 0.01208 ( 4) metal coordination : angle 2.73552 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8963 (tmtt) REVERT: B 63 GLU cc_start: 0.8801 (tt0) cc_final: 0.8278 (tt0) REVERT: B 92 ARG cc_start: 0.9452 (OUTLIER) cc_final: 0.8559 (tmm-80) REVERT: C 64 GLU cc_start: 0.8854 (tp30) cc_final: 0.8614 (tm-30) REVERT: D 43 LYS cc_start: 0.9331 (mmtm) cc_final: 0.8948 (tppt) REVERT: D 65 ASP cc_start: 0.9211 (t0) cc_final: 0.8950 (t0) REVERT: D 90 GLU cc_start: 0.8561 (mp0) cc_final: 0.8129 (mp0) REVERT: E 76 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8899 (mp10) REVERT: F 25 ASN cc_start: 0.9003 (OUTLIER) cc_final: 0.8476 (t0) REVERT: F 92 ARG cc_start: 0.9494 (OUTLIER) cc_final: 0.9051 (ttp80) REVERT: G 39 TYR cc_start: 0.8637 (m-80) cc_final: 0.7871 (m-80) REVERT: G 92 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: G 94 ASN cc_start: 0.9427 (OUTLIER) cc_final: 0.8981 (m-40) REVERT: H 65 ASP cc_start: 0.9240 (t0) cc_final: 0.8990 (t0) REVERT: H 68 GLU cc_start: 0.9145 (tp30) cc_final: 0.8485 (tp30) REVERT: H 102 GLU cc_start: 0.7925 (tp30) cc_final: 0.7580 (tp30) outliers start: 20 outliers final: 9 residues processed: 160 average time/residue: 0.1175 time to fit residues: 26.2817 Evaluate side-chains 163 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.052298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.037145 restraints weight = 73229.892| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.87 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13366 Z= 0.168 Angle : 0.632 10.963 19335 Z= 0.361 Chirality : 0.035 0.207 2229 Planarity : 0.004 0.051 1440 Dihedral : 30.383 114.846 4132 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.28 % Allowed : 26.14 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.29), residues: 840 helix: 2.13 (0.22), residues: 564 sheet: 0.92 (1.57), residues: 12 loop : -0.52 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.025 0.002 TYR G 57 PHE 0.007 0.001 PHE A 67 TRP 0.006 0.001 TRP M 25 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00372 (13362) covalent geometry : angle 0.63137 (19329) hydrogen bonds : bond 0.04328 ( 803) hydrogen bonds : angle 3.27842 ( 2016) metal coordination : bond 0.00787 ( 4) metal coordination : angle 2.12529 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1995.09 seconds wall clock time: 35 minutes 8.86 seconds (2108.86 seconds total)